Danny Baker's Christmas Hits (shown on Pick and Sky Arts on Christmas Day) played Rockin Around the Christmas Tree, thumbs-up to Rolf uncensored. Presumably it's so well-known that Mel and Kim's version contains the Two Little Boys reference, it was felt that omitting it would be more noticeable than not.
My own preference is the route that sites like TV Cream have taken - if something's 'archive', i.e. it existed pre-Yewtree and is an innocuous, non-offensive reference that doesn't make needless fun of a given victim or event, then just leave it as-is and people will recognise it comes from a different time. Sure, keep recent developments in mind when producing new content, but let the record stand where it stands.
Look at all the hoo-hah here on DS and elsewhere when potentially-mildly-offensive sequences are excised from The Simpsons, for instance, or the fuss every year over whether TV and radio stations will 'clean up' Fairytale of New York or let it fly (thankfully most airings of Fairytale I've been tuned into this year have left 'bum' and the rest untouched...)